I was in WDW for the marathon in 2003, and except for some areas blocked off that were not much of a hassle in Epcot and AK (those were the parks we went two on the actual day of the marathon), the marathon itself did not interfere at all with our vacation.
The overall crowds for the few days before and after the marathon were just as slow as you would expect in January, so it really didn't affect us at all.